Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted phylogenetic networks that has been extensively investigated in recent years. In this paper, we give a novel characterisation of a tree-child network $mathcal{R}$ in terms of cherry-picking sequences that are sequences on the leaves of $mathcal{R}$ and reduce it to a single vertex by repeatedly applying one of two reductions to its leaves. We show that our characterisation extends to unrooted tree-child networks which are mostly unexplored in the literature and, in turn, also offers a new approach to settling the computational complexity of deciding if an unrooted phylogenetic network can be oriented as a rooted tree-child network.
{"title":"Characterising rooted and unrooted tree-child networks","authors":"Janosch Döcker, Simone Linz","doi":"arxiv-2408.17105","DOIUrl":"https://doi.org/arxiv-2408.17105","url":null,"abstract":"Rooted phylogenetic networks are used by biologists to infer and represent\u0000complex evolutionary relationships between species that cannot be accurately\u0000explained by a phylogenetic tree. Tree-child networks are a particular class of\u0000rooted phylogenetic networks that has been extensively investigated in recent\u0000years. In this paper, we give a novel characterisation of a tree-child network\u0000$mathcal{R}$ in terms of cherry-picking sequences that are sequences on the\u0000leaves of $mathcal{R}$ and reduce it to a single vertex by repeatedly applying\u0000one of two reductions to its leaves. We show that our characterisation extends\u0000to unrooted tree-child networks which are mostly unexplored in the literature\u0000and, in turn, also offers a new approach to settling the computational\u0000complexity of deciding if an unrooted phylogenetic network can be oriented as a\u0000rooted tree-child network.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chiranjib Chaudhuri, Krishnendu Basak, M Suraj, Moiz Ahmed, Amit Kumar
This study uses Joint Species Distribution Models (JSDMs) and Deep Neural Networks (DNNs) to explore how wild carnivores and free-ranging dogs interact in the Udanti-Sitanadi Tiger Reserve (USTR) in Central India. The research focuses on key species like the Striped Hyena, Grey Wolf, Golden Jackal, and Indian Fox, revealing significant overlaps in habitat with free-ranging dogs, especially in densely populated areas like the Sitanadi region of the tiger reserve. These overlaps pose serious risks to wildlife through competition for resources, predation, and the spread of diseases. The study shows that the Striped Hyena prefers gentle slopes and forested areas, while the Grey Wolf tends to avoid cropland and thrives in regions with higher rainfall that supports a stable prey base. The Golden Jackal, more adaptable than the others, favors west-facing slopes and stable temperatures, whereas the Indian Fox is mainly found in the less disturbed, mountainous Kuladighat region. Additionally, the study highlights the potential impacts of climate change, predicting that the Grey Wolf could face habitat extinction under more severe scenarios. These findings underscore the urgent need for conservation strategies tailored to address both dog wild carnivore interactions and the growing challenges posed by climate change, focusing on protecting the critical habitats of vulnerable species like the Striped Hyena and Grey Wolf.
{"title":"Dogs on forest trails; Understanding ecology of Striped Hyena and wild Canids in the presence of free-ranging dogs in Udanti-Sitanadi Tiger Reserve, Central India using Joint Distribution and Deep Neural Networks","authors":"Chiranjib Chaudhuri, Krishnendu Basak, M Suraj, Moiz Ahmed, Amit Kumar","doi":"arxiv-2409.00185","DOIUrl":"https://doi.org/arxiv-2409.00185","url":null,"abstract":"This study uses Joint Species Distribution Models (JSDMs) and Deep Neural\u0000Networks (DNNs) to explore how wild carnivores and free-ranging dogs interact\u0000in the Udanti-Sitanadi Tiger Reserve (USTR) in Central India. The research\u0000focuses on key species like the Striped Hyena, Grey Wolf, Golden Jackal, and\u0000Indian Fox, revealing significant overlaps in habitat with free-ranging dogs,\u0000especially in densely populated areas like the Sitanadi region of the tiger\u0000reserve. These overlaps pose serious risks to wildlife through competition for\u0000resources, predation, and the spread of diseases. The study shows that the\u0000Striped Hyena prefers gentle slopes and forested areas, while the Grey Wolf\u0000tends to avoid cropland and thrives in regions with higher rainfall that\u0000supports a stable prey base. The Golden Jackal, more adaptable than the others,\u0000favors west-facing slopes and stable temperatures, whereas the Indian Fox is\u0000mainly found in the less disturbed, mountainous Kuladighat region.\u0000Additionally, the study highlights the potential impacts of climate change,\u0000predicting that the Grey Wolf could face habitat extinction under more severe\u0000scenarios. These findings underscore the urgent need for conservation\u0000strategies tailored to address both dog wild carnivore interactions and the\u0000growing challenges posed by climate change, focusing on protecting the critical\u0000habitats of vulnerable species like the Striped Hyena and Grey Wolf.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"128 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Krishnendu Basak, Chiranjib Chaudhuri, M Suraj, Moiz Ahmed
This study investigates the trophic cascades and habitat suitability in Udanti Sitnadi Tiger Reserve (USTR), highlighting the roles of apex predators, subordinate predators, and prey species in maintaining ecosystem balance. Using the Trophic Species Distribution Model (SDM), we explored prey-predator interactions and habitat suitability, revealing that tigers, due to prey depletion, increasingly rely on cattle, while leopards adapt by preying on smaller species. The study emphasizes the need for prey augmentation and habitat restoration to support apex predators. Additionally, climate change projections for 2021-2040 and 2081-2100 under CMIP6 scenarios SSP245 and SSP585 indicate significant regional habitat shifts, necessitating adaptive management strategies. Kuladighat is projected to face habitat contraction, while Sitanadi may experience habitat expansion. Effective conservation efforts such as habitat restoration, prey augmentation and predator recovery are the most important steps needed to maintain the purpose of a Tiger reserve and conservation potential of Udanti-Sonabeda Tiger Conservation Unit (TCU). To achieve these dynamics, focusing on community participation, anti-poaching measures, and scientific recommendations are the most crucial components to focus on. This comprehensive analysis underscores the critical role of targeted conservation activities in prey-depleted landscapes to ensure the long-term survival of tigers and the overall health of forest ecosystems, enhancing biodiversity and mitigating human-wildlife conflicts in USTR.
{"title":"Trophic Cascades and Habitat Suitability in Udanti Sitnadi Tiger Reserve: Impacts of Prey Depletion and Climate Change on Predator Prey Dynamics","authors":"Krishnendu Basak, Chiranjib Chaudhuri, M Suraj, Moiz Ahmed","doi":"arxiv-2409.00193","DOIUrl":"https://doi.org/arxiv-2409.00193","url":null,"abstract":"This study investigates the trophic cascades and habitat suitability in\u0000Udanti Sitnadi Tiger Reserve (USTR), highlighting the roles of apex predators,\u0000subordinate predators, and prey species in maintaining ecosystem balance. Using\u0000the Trophic Species Distribution Model (SDM), we explored prey-predator\u0000interactions and habitat suitability, revealing that tigers, due to prey\u0000depletion, increasingly rely on cattle, while leopards adapt by preying on\u0000smaller species. The study emphasizes the need for prey augmentation and\u0000habitat restoration to support apex predators. Additionally, climate change\u0000projections for 2021-2040 and 2081-2100 under CMIP6 scenarios SSP245 and SSP585\u0000indicate significant regional habitat shifts, necessitating adaptive management\u0000strategies. Kuladighat is projected to face habitat contraction, while Sitanadi\u0000may experience habitat expansion. Effective conservation efforts such as\u0000habitat restoration, prey augmentation and predator recovery are the most\u0000important steps needed to maintain the purpose of a Tiger reserve and\u0000conservation potential of Udanti-Sonabeda Tiger Conservation Unit (TCU). To\u0000achieve these dynamics, focusing on community participation, anti-poaching\u0000measures, and scientific recommendations are the most crucial components to\u0000focus on. This comprehensive analysis underscores the critical role of targeted\u0000conservation activities in prey-depleted landscapes to ensure the long-term\u0000survival of tigers and the overall health of forest ecosystems, enhancing\u0000biodiversity and mitigating human-wildlife conflicts in USTR.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Baptiste Sorin-Dupont, Antoine Poyard, Sebastien Assie, Sebastien Picault, Pauline Ezanno
The overuse of antibiotics has become a major global concern due to its role in diminishing treatment effectiveness and positively selecting antibiotic-resistant bacterial strains. This issue is particularly important in the beef cattle sector, where Bovine Respiratory Diseases (BRD) impose significant economic and welfare burdens. BRD are complex, multifactorial conditions primarily affecting young calves and feedlot cattle, caused by a combination of viral and bacterial pathogens, environmental factors, and stressors. Despite efforts to reduce antimicrobial use (AMU), the cattle production system remains heavily reliant on antibiotics to control BRD, often through the implementation of collective treatments to prevent outbreaks. This study aimed at evaluating the impact of various treatment practices on the spread of BRD, specifically focusing on criteria for implementing collective treatments. Using a mechanistic stochastic model, we simulated the spread of textit{Mannheimia haemolytica} in a multi-pen fattening operation under sixteen different scenarios, considering pen composition, individual risk levels, and treatment strategies. Our findings suggest that an alternative criterion for collective treatments based on the speed of the disease spread, could reduce BRD incidence and AMU more effectively than conventional methods. This research highlights the importance of responsible treatment practices and the potential benefits of novel criteria for collective treatment strategies in improving animal health. Moreover, it emphasizes the need for transparency on the exposure to risk factors along the production chain.
{"title":"Individual or collective treatments: how to target antimicrobial use to limit the spread of respiratory pathogens among beef cattle?","authors":"Baptiste Sorin-Dupont, Antoine Poyard, Sebastien Assie, Sebastien Picault, Pauline Ezanno","doi":"arxiv-2408.16269","DOIUrl":"https://doi.org/arxiv-2408.16269","url":null,"abstract":"The overuse of antibiotics has become a major global concern due to its role\u0000in diminishing treatment effectiveness and positively selecting\u0000antibiotic-resistant bacterial strains. This issue is particularly important in\u0000the beef cattle sector, where Bovine Respiratory Diseases (BRD) impose\u0000significant economic and welfare burdens. BRD are complex, multifactorial\u0000conditions primarily affecting young calves and feedlot cattle, caused by a\u0000combination of viral and bacterial pathogens, environmental factors, and\u0000stressors. Despite efforts to reduce antimicrobial use (AMU), the cattle\u0000production system remains heavily reliant on antibiotics to control BRD, often\u0000through the implementation of collective treatments to prevent outbreaks. This\u0000study aimed at evaluating the impact of various treatment practices on the\u0000spread of BRD, specifically focusing on criteria for implementing collective\u0000treatments. Using a mechanistic stochastic model, we simulated the spread of\u0000textit{Mannheimia haemolytica} in a multi-pen fattening operation under\u0000sixteen different scenarios, considering pen composition, individual risk\u0000levels, and treatment strategies. Our findings suggest that an alternative\u0000criterion for collective treatments based on the speed of the disease spread,\u0000could reduce BRD incidence and AMU more effectively than conventional methods.\u0000This research highlights the importance of responsible treatment practices and\u0000the potential benefits of novel criteria for collective treatment strategies in\u0000improving animal health. Moreover, it emphasizes the need for transparency on\u0000the exposure to risk factors along the production chain.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.
{"title":"Transformations to simplify phylogenetic networks","authors":"Johanna Heiss, Daniel H. Huson, Mike Steel","doi":"arxiv-2408.16156","DOIUrl":"https://doi.org/arxiv-2408.16156","url":null,"abstract":"The evolutionary relationships between species are typically represented in\u0000the biological literature by rooted phylogenetic trees. However, a tree fails\u0000to capture ancestral reticulate processes, such as the formation of hybrid\u0000species or lateral gene transfer events between lineages, and so the history of\u0000life is more accurately described by a rooted phylogenetic network.\u0000Nevertheless, phylogenetic networks may be complex and difficult to interpret,\u0000so biologists sometimes prefer a tree that summarises the central tree-like\u0000trend of evolution. In this paper, we formally investigate methods for\u0000transforming an arbitrary phylogenetic network into a tree (on the same set of\u0000leaves) and ask which ones (if any) satisfy a simple consistency condition.\u0000This consistency condition states that if we add additional species into a\u0000phylogenetic network (without otherwise changing this original network) then\u0000transforming this enlarged network into a rooted phylogenetic tree induces the\u0000same tree on the original set of species as transforming the original network.\u0000We show that the LSA (lowest stable ancestor) tree method satisfies this\u0000consistency property, whereas several other commonly used methods (and a new\u0000one we introduce) do not. We also briefly consider transformations that convert\u0000arbitrary phylogenetic networks to another simpler class, namely normal\u0000networks.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In the present paper, our goal is to establish a framework for the mathematical modelling and the analysis of the spread of an epidemic in a large population commuting regularly, typically along a time-periodic pattern, as is roughly speaking the case in populous urban center. We consider a large number of distinct homogeneous groups of individuals of various sizes, called subpopulations, and focus on the modelling of the changing conditions of their mixing along time and of the induced disease transmission. We propose a general class of models in which the 'force of infection' plays a central role, which attempts to 'reconcile' the classical modelling approaches in mathematical epidemiology, based on compartmental models, with some widely used analysis results (including those by P. van den Driessche and J. Watmough in 2002), established for apparently less structured systems of nonlinear ordinary-differential equations. We take special care in explaining the modelling approach in details, and provide analysis results that allow to compute or estimate the value of the basic reproduction number for such general periodic epidemic systems.
在本文中，我们的目标是建立一个数学建模框架，并分析流行病在大量人口中的传播情况，这些人口通常是按时间周期规律定期通勤的，人口众多的城市中心就是这种情况。我们考虑了大量由不同规模的个体组成的不同同质群体（称为亚群体），并重点研究了这些群体的混杂条件随时间的变化以及诱发疾病传播的模型。我们提出了一类以 "感染力 "为核心的通用模型，试图 "调和 "数学流行病学中以分室模型为基础的经典建模方法和一些广泛使用的分析结果（包括 P. van den Driessche 和 J. Watmough 在 2002 年提出的分析结果），这些分析结果是针对结构显然不太严谨的非线性常微分方程系统建立的。我们特别注意详细解释建模方法，并提供分析结果，以便计算或估计这类一般周期性流行病系统的基本繁殖数值。
{"title":"A framework for the modelling and the analysis of epidemiological spread in commuting populations","authors":"Pierre-Alexandre BlimanMUSCLEES, Boureima SangaréUNB, Assane SavadogoMUSCLEES, UNB","doi":"arxiv-2408.15634","DOIUrl":"https://doi.org/arxiv-2408.15634","url":null,"abstract":"In the present paper, our goal is to establish a framework for the\u0000mathematical modelling and the analysis of the spread of an epidemic in a large\u0000population commuting regularly, typically along a time-periodic pattern, as is\u0000roughly speaking the case in populous urban center. We consider a large number\u0000of distinct homogeneous groups of individuals of various sizes, called\u0000subpopulations, and focus on the modelling of the changing conditions of their\u0000mixing along time and of the induced disease transmission. We propose a general\u0000class of models in which the 'force of infection' plays a central role, which\u0000attempts to 'reconcile' the classical modelling approaches in mathematical\u0000epidemiology, based on compartmental models, with some widely used analysis\u0000results (including those by P. van den Driessche and J. Watmough in 2002),\u0000established for apparently less structured systems of nonlinear\u0000ordinary-differential equations. We take special care in explaining the\u0000modelling approach in details, and provide analysis results that allow to\u0000compute or estimate the value of the basic reproduction number for such general\u0000periodic epidemic systems.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"8995 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The reticulation number for a set of trees is defined as the minimum number of reticulations in a phylogenetic network that displays those trees. A mathematical problem is bounding the reticulation number for multiple trees over a fixed number of taxa. While this problem has been extensively studied for two trees, much less is known about the upper bounds on the reticulation numbers for three or more arbitrary trees. In this paper, we present a few non-trivial upper bounds on reticulation numbers for three or more trees.
{"title":"Bounding the number of reticulation events for displaying multiple trees in a phylogenetic network","authors":"Yufeng Wu, Louxin Zhang","doi":"arxiv-2408.14202","DOIUrl":"https://doi.org/arxiv-2408.14202","url":null,"abstract":"Reconstructing a parsimonious phylogenetic network that displays multiple\u0000phylogenetic trees is an important problem in theory of phylogenetics, where\u0000the complexity of the inferred networks is measured by reticulation numbers.\u0000The reticulation number for a set of trees is defined as the minimum number of\u0000reticulations in a phylogenetic network that displays those trees. A\u0000mathematical problem is bounding the reticulation number for multiple trees\u0000over a fixed number of taxa. While this problem has been extensively studied\u0000for two trees, much less is known about the upper bounds on the reticulation\u0000numbers for three or more arbitrary trees. In this paper, we present a few\u0000non-trivial upper bounds on reticulation numbers for three or more trees.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"402 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
What makes living things special is how they manage matter, energy, and entropy. A general theory of organismal metabolism should therefore be quantified in these three currencies while capturing the unique way they flow between individuals and their environments. We argue that such a theory has quietly arrived -- 'Dynamic Energy Budget' (DEB) theory -- which conceptualises organisms as a series of macrochemical reactions that use energy to transform food into structured biomass and bioproducts while producing entropy. We show that such conceptualisation is deeply rooted in thermodynamic principles and that, with the help of a small set of biological assumptions, it underpins the emergence of fundamental ecophysiological phenomena, most notably the three-quarter power scaling of metabolism. Building on the subcellular nature of the theory, we unveil the eco-evolutionary relevance of coarse-graining biomass into qualitatively distinct, stoichiometricially fixed pools with implicitly regulated dynamics based on surface area-volume relations. We also show how generalised enzymes called 'synthesising units' and an information-based state variable called 'maturity' capture transitions between ecological and physiological metabolic interactions, and thereby transitions between unicellular and multicellular metabolic organisation. Formal theoretical frameworks make the constraints imposed by the laws of nature explicit, which in turn leads to better research hypotheses and avoids errors in reasoning. DEB theory uniquely applies thermodynamic formalism to organismal metabolism, linking biological processes across different scales through the transformation of matter and energy, the production of entropy, and the exchange of information. We propose ways in which the theory can inform trans-disciplinary efforts at the frontiers of the life sciences.
{"title":"The untapped power of a general theory of organismal metabolism","authors":"Marko Jusup, Michael R. Kearney","doi":"arxiv-2408.13998","DOIUrl":"https://doi.org/arxiv-2408.13998","url":null,"abstract":"What makes living things special is how they manage matter, energy, and\u0000entropy. A general theory of organismal metabolism should therefore be\u0000quantified in these three currencies while capturing the unique way they flow\u0000between individuals and their environments. We argue that such a theory has\u0000quietly arrived -- 'Dynamic Energy Budget' (DEB) theory -- which conceptualises\u0000organisms as a series of macrochemical reactions that use energy to transform\u0000food into structured biomass and bioproducts while producing entropy. We show\u0000that such conceptualisation is deeply rooted in thermodynamic principles and\u0000that, with the help of a small set of biological assumptions, it underpins the\u0000emergence of fundamental ecophysiological phenomena, most notably the\u0000three-quarter power scaling of metabolism. Building on the subcellular nature\u0000of the theory, we unveil the eco-evolutionary relevance of coarse-graining\u0000biomass into qualitatively distinct, stoichiometricially fixed pools with\u0000implicitly regulated dynamics based on surface area-volume relations. We also\u0000show how generalised enzymes called 'synthesising units' and an\u0000information-based state variable called 'maturity' capture transitions between\u0000ecological and physiological metabolic interactions, and thereby transitions\u0000between unicellular and multicellular metabolic organisation. Formal\u0000theoretical frameworks make the constraints imposed by the laws of nature\u0000explicit, which in turn leads to better research hypotheses and avoids errors\u0000in reasoning. DEB theory uniquely applies thermodynamic formalism to organismal\u0000metabolism, linking biological processes across different scales through the\u0000transformation of matter and energy, the production of entropy, and the\u0000exchange of information. We propose ways in which the theory can inform\u0000trans-disciplinary efforts at the frontiers of the life sciences.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The concepts of spread and spread dimension of a metric space were introduced by Willerton in the context of quantifying biodiversity of ecosystems. In previous work, we developed the theoretical basis for applications of spread dimension as an intrinsic dimension estimator. In this paper we introduce the pseudo spread dimension which is an efficient approximation of spread dimension, and we derive a formula for the standard error associated with this approximation.
{"title":"Efficiently Approximating Spread Dimension with High Confidence","authors":"Kevin Dunne","doi":"arxiv-2408.14590","DOIUrl":"https://doi.org/arxiv-2408.14590","url":null,"abstract":"The concepts of spread and spread dimension of a metric space were introduced\u0000by Willerton in the context of quantifying biodiversity of ecosystems. In\u0000previous work, we developed the theoretical basis for applications of spread\u0000dimension as an intrinsic dimension estimator. In this paper we introduce the\u0000pseudo spread dimension which is an efficient approximation of spread\u0000dimension, and we derive a formula for the standard error associated with this\u0000approximation.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ramsey et al. report on the characteristics and temporal distribution of an interesting vibrational signal that they term the whooping signal, primarily based upon a long-term study of vibrations recorded by accelerometers placed inside two honey bee (Apis mellifera) colonies, one in France and one in the United Kingdom. The goal of the study, the long-term automated recording and analysis of honey bee vibrational signaling, is worthwhile. However, we believe that some of the conclusions drawn by the authors are not well supported, given the evidence.
{"title":"The complex world of honey bee vibrational signaling: A response to Ramsey et al. (2017)","authors":"Heather C Bell, Parry M Keitzman, James C Nieh","doi":"arxiv-2408.14430","DOIUrl":"https://doi.org/arxiv-2408.14430","url":null,"abstract":"Ramsey et al. report on the characteristics and temporal distribution of an\u0000interesting vibrational signal that they term the whooping signal, primarily\u0000based upon a long-term study of vibrations recorded by accelerometers placed\u0000inside two honey bee (Apis mellifera) colonies, one in France and one in the\u0000United Kingdom. The goal of the study, the long-term automated recording and\u0000analysis of honey bee vibrational signaling, is worthwhile. However, we believe\u0000that some of the conclusions drawn by the authors are not well supported, given\u0000the evidence.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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